mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 40 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 69.0% | 14.7 / 14.9 | 32 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 53.3% | ‑2.8 / 15.2 | 16 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,951,092 | 0 | G | T | 53.3% | 11.8 / 19.2 | 15 | intergenic (‑56/+139) | PP_3486/PP_3487 | cytochrome c/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.2% | 55.3 / 234.8 | 160 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.8% | 34.0 / 188.2 | 133 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 48.1% | 8.5 / 12.8 | 33 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,653,618 | 0 | C | A | 47.6% | 5.1 / 11.4 | 21 | intergenic (+57/‑68) | PP_2325/PP_2326 | 2‑dehydropantoate 2‑reductase/universal stress protein |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 47.1% | ‑0.1 / 10.0 | 17 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 45.8% | 35.6 / 160.0 | 118 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 45.7% | 2.8 / 14.7 | 35 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 44.4% | 27.1 / 14.3 | 37 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 36.4% | 129.6 / 121.8 | 133 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 33.3% | 23.4 / 11.1 | 33 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 31.9% | 55.5 / 11.9 | 47 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 30.9% | 78.3 / 12.0 | 55 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 697,128 | 0 | T | G | 30.8% | 40.0 / 10.2 | 39 | intergenic (+55/‑696) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,442,126 | 0 | C | G | 30.0% | 40.4 / 11.7 | 30 | R15R (CGG→CGC) | rluE | 23S rRNA pseudouridine(2457) synthase |
| * | NC_002947_CJ‑RC | 3,941,240 | 0 | G | C | 28.2% | 153.4 / 11.8 | 71 | G106G (GGC→GGG) | PP_3476 | type II secretion system protein G |
| * | NC_002947_CJ‑RC | 5,754,548 | 0 | C | A | 27.9% | 83.5 / 11.6 | 48 | intergenic (‑171/‑300) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 5,181,205 | 0 | C | G | 27.5% | 116.2 / 12.6 | 52 | intergenic (‑179/+13) | PP_4556/PP_4557 | hypothetical protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 88 (1.040) | 25 (0.330) | 20/256 | 5.0 | 23.1% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 89 (1.190) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 82 (0.970) | 20 (0.270) | 17/250 | 5.7 | 35.5% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 2 (0.030) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 18 (0.230) | 18/266 | 5.8 | 41.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 48 (0.620) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.470) | 20 (0.240) | 19/280 | 5.9 | 32.1% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 46 (0.560) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 11 (0.130) | 18 (0.280) | 11/220 | 6.8 | 41.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 43 (0.670) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 16 (0.190) +GCC |
16/284 | 7.0 | 84.5% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 14 (0.170) +CGGG |
13/282 | 8.0 | 100% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 16 (0.190) | 19 (0.230) | 13/284 | 8.1 | 50.2% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 22 (0.260) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 56 (0.660) | 12 (0.150) | 12/274 | 8.2 | 17.3% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 62 (0.770) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991572 | 57 (0.670) | 11 (0.140) | 11/274 | 8.6 | 15.0% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991794 = | 71 (0.890) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||